1SPA
 
 | | ROLE OF ASP222 IN THE CATALYTIC MECHANISM OF ESCHERICHIA COLI ASPARTATE AMINOTRANSFERASE: THE AMINO ACID RESIDUE WHICH ENHANCES THE FUNCTION OF THE ENZYME-BOUND COENZYME PYRIDOXAL 5'-PHOSPHATE | | Descriptor: | ASPARTATE AMINOTRANSFERASE, N-METHYL-4-DEOXY-4-AMINO-PYRIDOXAL-5-PHOSPHATE | | Authors: | Hinoue, Y, Yano, T, Metzler, D.E, Miyahara, I, Hirotsu, K, Kagamiyama, H. | | Deposit date: | 1993-01-26 | | Release date: | 1993-10-31 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Role of Asp222 in the catalytic mechanism of Escherichia coli aspartate aminotransferase: the amino acid residue which enhances the function of the enzyme-bound coenzyme pyridoxal 5'-phosphate.
Biochemistry, 31, 1992
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1CZC
 | | ASPARTATE AMINOTRANSFERASE MUTANT ATB17/139S/142N WITH GLUTARIC ACID | | Descriptor: | GLUTARIC ACID, PROTEIN (ASPARTATE AMINOTRANSFERASE), PYRIDOXAL-5'-PHOSPHATE | | Authors: | Okamoto, A, Oue, S, Yano, T, Kagamiyama, H. | | Deposit date: | 1999-09-02 | | Release date: | 2000-02-28 | | Last modified: | 2023-08-09 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Cocrystallization of a mutant aspartate aminotransferase with a C5-dicarboxylic substrate analog: structural comparison with the enzyme-C4-dicarboxylic analog complex.
J.Biochem.(Tokyo), 127, 2000
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1CZE
 | | ASPARTATE AMINOTRANSFERASE MUTANT ATB17/139S/142N WITH SUCCINIC ACID | | Descriptor: | ASPARTATE AMINOTRANSFERASE, PYRIDOXAL-5'-PHOSPHATE, SUCCINIC ACID | | Authors: | Okamoto, A, Oue, S, Yano, T, Kagamiyama, H. | | Deposit date: | 1999-09-02 | | Release date: | 2000-02-28 | | Last modified: | 2023-08-09 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Cocrystallization of a mutant aspartate aminotransferase with a C5-dicarboxylic substrate analog: structural comparison with the enzyme-C4-dicarboxylic analog complex.
J.Biochem.(Tokyo), 127, 2000
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3K8U
 | | Crystal Structure of the Peptidase Domain of Streptococcus ComA, a Bi-functional ABC Transporter Involved in Quorum Sensing Pathway | | Descriptor: | Putative ABC transporter, ATP-binding protein ComA | | Authors: | Ishii, S, Yano, T, Ebihara, A, Okamoto, A, Manzoku, M, Hayashi, H. | | Deposit date: | 2009-10-14 | | Release date: | 2010-02-23 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Crystal structure of the peptidase domain of Streptococcus ComA, a bifunctional ATP-binding cassette transporter involved in the quorum-sensing pathway
J.Biol.Chem., 285, 2010
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8H1F
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8H1E
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8H1G
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1YOO
 | | ASPARTATE AMINOTRANSFERASE MUTANT ATB17 WITH ISOVALERIC ACID | | Descriptor: | ASPARTATE AMINOTRANSFERASE, ISOVALERIC ACID, PYRIDOXAL-5'-PHOSPHATE | | Authors: | Oue, S, Okamoto, A, Yano, T, Kagamiyama, H. | | Deposit date: | 1998-06-26 | | Release date: | 1999-02-02 | | Last modified: | 2023-08-09 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Redesigning the substrate specificity of an enzyme by cumulative effects of the mutations of non-active site residues.
J.Biol.Chem., 274, 1999
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2VPX
 | | Polysulfide reductase with bound quinone (UQ1) | | Descriptor: | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE, HYPOTHETICAL MEMBRANE SPANNING PROTEIN, IRON/SULFUR CLUSTER, ... | | Authors: | Jormakka, M, Yokoyama, K, Yano, T, Tamakoshi, M, Akimoto, S, Shimamura, T, Curmi, P, Iwata, S. | | Deposit date: | 2008-03-09 | | Release date: | 2008-06-10 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (3.1 Å) | | Cite: | Molecular Mechanism of Energy Conservation in Polysulfide Respiration.
Nat.Struct.Mol.Biol., 15, 2008
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2VPY
 | | Polysulfide reductase with bound quinone inhibitor, pentachlorophenol (PCP) | | Descriptor: | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE, HYPOTHETICAL MEMBRANE SPANNING PROTEIN, IRON/SULFUR CLUSTER, ... | | Authors: | Jormakka, M, Yokoyama, K, Yano, T, Tamakoshi, M, Akimoto, S, Shimamura, T, Curmi, P, Iwata, S. | | Deposit date: | 2008-03-09 | | Release date: | 2008-06-10 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Molecular Mechanism of Energy Conservation in Polysulfide Respiration.
Nat.Struct.Mol.Biol., 15, 2008
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2VPW
 | | Polysulfide reductase with bound menaquinone | | Descriptor: | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE, HYPOTHETICAL MEMBRANE SPANNING PROTEIN, IRON/SULFUR CLUSTER, ... | | Authors: | Jormakka, M, Yokoyama, K, Yano, T, Tamakoshi, M, Akimoto, S, Shimamura, T, Curmi, P, Iwata, S. | | Deposit date: | 2008-03-09 | | Release date: | 2008-06-10 | | Last modified: | 2019-02-06 | | Method: | X-RAY DIFFRACTION (3.1 Å) | | Cite: | Molecular Mechanism of Energy Conservation in Polysulfide Respiration.
Nat.Struct.Mol.Biol., 15, 2008
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5B42
 | | Crystal structure of the C-terminal endonuclease domain of Aquifex aeolicus MutL. | | Descriptor: | CADMIUM ION, DI(HYDROXYETHYL)ETHER, DNA mismatch repair protein MutL | | Authors: | Fukui, K, Baba, S, Kumasaka, T, Yano, T. | | Deposit date: | 2016-03-30 | | Release date: | 2016-07-13 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.35 Å) | | Cite: | Structural Features and Functional Dependency on beta-Clamp Define Distinct Subfamilies of Bacterial Mismatch Repair Endonuclease MutL
J.Biol.Chem., 291, 2016
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5H45
 | | Crystal structure of the C-terminal Lon protease-like domain of Thermus thermophilus RadA/Sms | | Descriptor: | DNA repair protein RadA | | Authors: | Inoue, M, Fukui, K, Fujii, Y, Nakagawa, N, Yano, T, Kuramitsu, S, Masui, R. | | Deposit date: | 2016-10-30 | | Release date: | 2017-05-03 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | The Lon protease-like domain in the bacterial RecA paralog RadA is required for DNA binding and repair.
J. Biol. Chem., 292, 2017
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7VUF
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7VUK
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5XE9
 | | Crystal Structure of the Complex of the Peptidase Domain of Streptococcus mutans ComA with a Small Molecule Inhibitor. | | Descriptor: | Putative ABC transporter, ATP-binding protein ComA, [(1~{S},2~{R},4~{S},5~{R})-5-[5-(4-methoxyphenyl)-2-methyl-pyrazol-3-yl]-1-azabicyclo[2.2.2]octan-2-yl]methyl ~{N}-propylcarbamate | | Authors: | Ishii, S, Fukui, K, Yokoshima, S, Kumagai, K, Beniyama, Y, Kodama, T, Fukuyama, T, Okabe, T, Nagano, T, Kojima, H, Yano, T. | | Deposit date: | 2017-04-03 | | Release date: | 2017-06-28 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (3.101 Å) | | Cite: | High-throughput Screening of Small Molecule Inhibitors of the Streptococcus Quorum-sensing Signal Pathway
Sci Rep, 7, 2017
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5XE8
 | | Crystal Structure of the Peptidase Domain of Streptococcus mutans ComA | | Descriptor: | DI(HYDROXYETHYL)ETHER, Putative ABC transporter, ATP-binding protein ComA | | Authors: | Ishii, S, Fukui, K, Yokoshima, S, Kumagai, K, Beniyama, Y, Kodama, T, Fukuyama, T, Okabe, T, Nagano, T, Kojima, H, Yano, T. | | Deposit date: | 2017-04-03 | | Release date: | 2017-06-28 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (3.1 Å) | | Cite: | High-throughput Screening of Small Molecule Inhibitors of the Streptococcus Quorum-sensing Signal Pathway
Sci Rep, 7, 2017
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8GUH
 | | Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with Tris | | Descriptor: | 1,2-ETHANEDIOL, Serine palmitoyltransferase, [4-[[[2-(hydroxymethyl)-1,3-bis(oxidanyl)propan-2-yl]amino]methyl]-6-methyl-5-oxidanyl-pyridin-3-yl]methyl dihydrogen phosphate | | Authors: | Murakami, T, Takahashi, A, Katayama, A, Miyahara, I, Kamiya, N, Ikushiro, H, Yano, T. | | Deposit date: | 2022-09-12 | | Release date: | 2023-07-19 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Crystal structure of Sphingobacterium multivorum serine palmitoyltransferase complexed with tris(hydroxymethyl)aminomethane.
Acta Crystallogr.,Sect.F, 78, 2022
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8H1W
 | | Serine Palmitoyltransferase from Sphingobacterium multivorum | | Descriptor: | 1,2-ETHANEDIOL, Serine palmitoyltransferase | | Authors: | Takahashi, A, Murakami, T, Katayama, A, Miyahara, I, Kamiya, N, Ikushiro, H, Yano, T. | | Deposit date: | 2022-10-04 | | Release date: | 2023-08-16 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (1.4 Å) | | Cite: | Structural insights into the substrate recognition of serine palmitoyltransferase from Sphingobacterium multivorum.
J.Biol.Chem., 299, 2023
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8H1Y
 | | Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with L-homoserine | | Descriptor: | (2~{S})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-4-oxidanyl-butanoic acid, 1,2-ETHANEDIOL, Serine palmitoyltransferase | | Authors: | Murakami, T, Takahashi, A, Katayama, A, Miyahara, I, Kamiya, N, Ikushiro, H, Yano, T. | | Deposit date: | 2022-10-04 | | Release date: | 2023-08-16 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | Structural insights into the substrate recognition of serine palmitoyltransferase from Sphingobacterium multivorum.
J.Biol.Chem., 299, 2023
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8H21
 | | Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with L-alanine | | Descriptor: | 1,2-ETHANEDIOL, 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-PROPIONIC ACID, Serine palmitoyltransferase | | Authors: | Murakami, T, Takahashi, A, Katayama, A, Miyahara, I, Kamiya, N, Ikushiro, H, Yano, T. | | Deposit date: | 2022-10-04 | | Release date: | 2023-08-16 | | Method: | X-RAY DIFFRACTION (1.54 Å) | | Cite: | Structural insights into the substrate recognition of serine palmitoyltransferase from Sphingobacterium multivorum.
J.Biol.Chem., 299, 2023
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8H29
 | | Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with L-threonine | | Descriptor: | 1,2-ETHANEDIOL, N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-threonine, Serine palmitoyltransferase | | Authors: | Murakami, T, Takahashi, A, Katayama, A, Miyahara, I, Kamiya, N, Ikushiro, H, Yano, T. | | Deposit date: | 2022-10-05 | | Release date: | 2023-08-16 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Structural insights into the substrate recognition of serine palmitoyltransferase from Sphingobacterium multivorum.
J.Biol.Chem., 299, 2023
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8H1Q
 | | Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with L-serine | | Descriptor: | 1,2-ETHANEDIOL, Serine palmitoyltransferase, [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE | | Authors: | Murakami, T, Takahashi, A, Katayama, A, Miyahara, I, Kamiya, N, Ikushiro, H, Yano, T. | | Deposit date: | 2022-10-03 | | Release date: | 2023-08-16 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Structural insights into the substrate recognition of serine palmitoyltransferase from Sphingobacterium multivorum.
J.Biol.Chem., 299, 2023
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8H20
 | | Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with Glycine | | Descriptor: | 1,2-ETHANEDIOL, N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE], Serine palmitoyltransferase | | Authors: | Murakami, T, Takahashi, A, Katayama, A, Miyahara, I, Kamiya, N, Ikushiro, H, Yano, T. | | Deposit date: | 2022-10-04 | | Release date: | 2023-08-16 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Structural insights into the substrate recognition of serine palmitoyltransferase from Sphingobacterium multivorum.
J.Biol.Chem., 299, 2023
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3VX4
 | | Crystal Structure of the Nucleotide-Binding Domain of S. mutans ComA, a Bifunctional ATP-binding Cassette Transporter Involved in the Quorum-sensing Pathway | | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, Putative ABC transporter, ... | | Authors: | Ishii, S, Yano, T, Okamoto, A, Murakawa, T, Hayashi, H. | | Deposit date: | 2012-09-11 | | Release date: | 2013-04-17 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.69 Å) | | Cite: | Boundary of the Nucleotide-Binding Domain of Streptococcus ComA Based on Functional and Structural Analysis
Biochemistry, 52, 2013
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